I don't really see a downside either, except logging out and in into the Kobo site or Desktop app whenever you need your previous account for some reason.
You can also "delete" all your previous purchases from the kobo site. The delete would only mean deleting the books from your "my reading" list, and the books will go into "archived." They won't sync to your device from there. That way, you could always choose to sync one of the books anyway if you'd suddenly decide you want to re-read something, of if kepub reading would change in some way that you'd prefer to use kepubs to sideloaded epubs.